Commit 3a016d03 authored by Mohammed Tanash's avatar Mohammed Tanash
Browse files

Merge branch 'AddExamples' into 'master'

Add Examples repo to the website

See merge request !254
parents 35f2fd24 b164ee24
! EXAM30.
! Test of water EFP ... formamide/three water complex
!
! FINAL E= -169.0085355753 after 12 iterations
! RMS gradient=0.008157643
!
! The geometry below combines a computed gas phase
! structure for formamide, with three waters located
! in a cylic fashion whose positions approximate the
! minimum structure of W.Chen and M.S.Gordon. This
! approximate structure lies about 11 mHartree above
! the actual minimum.
!
$contrl scftyp=rhf runtyp=gradient coord=zmt $end
$system timlim=2 $end
$basis gbasis=dh npfunc=1 ndfunc=1 $end
$data
formamide with three effective fragment waters
C1
C
O 1 rCO
N 1 rCN 2 aNCO
H 3 rNHa 1 aCNHa 2 0.0
H 3 rNHb 1 aCNHb 2 180.0
H 1 rCH 2 aHCO 4 180.0
rCO=1.1962565
rCN=1.3534065
rNHa=0.9948420
rNHb=0.9921367
rCH=1.0918368
aNCO=124.93384
aCNHa=119.16000
aCNHb=121.22477
aHCO=122.30822
$end
$efrag
coord=int
fragname=H2ORHF
O1 4 1.926 3 175.0 1 180.0
H2 7 0.9438636 4 117.4 3 -175.0
H3 7 0.9438636 8 106.70327 4 95.0
fragname=H2ORHF
O1 8 1.901 7 175.0 4 0.0
H2 10 0.9438636 8 110.0 4 -5.0
H3 10 0.9438636 11 106.70327 8 -95.0
fragname=H2ORHF
H2 2 1.951 1 150.0 3 0.0
O1 13 0.9438636 2 177.0 3 0.0
H3 14 0.9438636 13 106.70327 3 140.0
$end
#!/bin/bash
#SBATCH -J gamess
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=8
#SBATCH --mem-per-cpu=2048
#SBATCH --time=02:00:00
#SBATCH --error=TestJob.%J.stderr
#SBATCH --output=TestJob.%J.stdout
module load compiler/intel/19 openmpi/2.0
module load gamess/20190930R2
nodelist > ./PBS_NODEFILE
echo $SLURM_JOB_ID > ./jobid
export NCPUS=`wc -l < ./PBS_NODEFILE`
rm -rf ${WORK}/scr/
mkdir -p ${WORK}/scr/
rungms exam30 00 $NCPUS $SLURM_NTASKS_PER_NODE >& exam30.log
cp ${WORK}/scr/* .
+++
title = "Gamess Example"
weight = "100"
+++
Gamess Example
--------------------------------------
{{< readfile file="content/submitting_jobs/app_specific/job-examples/gamess/README.md" markdown="true" >}}
{{%attachments title="Related files" style="orange" /%}}
#!/bin/bash
#SBATCH -J g09
#SBATCH --nodes=1 --ntasks-per-node=4
#SBATCH --mem-per-cpu=2000
#SBATCH --time=10:00:00
#SBATCH --partition=batch
#SBATCH --error=TestJob.stderr
#SBATCH --output=TestJob.stdout
nodelist > ./machines.LINUX
echo $SLURM_JOB_ID > ./jobid
module load gaussian/09/RevE
source ${g09root}/g09/bsd/g09.profile
export GAUSS_SCRDIR=$TMPDIR
g09 test_g98.com
%nprocs=4
#P RHF/6-31G** scf=direct test prop=fit
Gaussian Test Job 178:
TATB rhf/6-31g**//hf/6-31g**
Energy with tight cutoffs would be -1006.2213391, is -1006.2213170 with
default cutoffs
0,1
X
C,1,RC1
C,1,RC2,2,60.
C,1,RC1,3,60.,2,180.,0
C,1,RC2,4,60.,3,180.,0
C,1,RC1,5,60.,4,180.,0
C,1,RC2,6,60.,5,180.,0
X,2,1.,1,90.,3,0.,0
X,3,1.,1,90.,4,0.,0
X,4,1.,1,90.,5,0.,0
X,5,1.,1,90.,6,0.,0
X,6,1.,1,90.,7,0.,0
X,7,1.,1,90.,2,0.,0
N,2,RCN1,8,90.,1,180.,0
O,14,RNO,2,A1,8,0.,0
O,14,RNO,2,A1,8,180.,0
N,4,RCN1,10,90.,1,180.,0
O,17,RNO,4,A1,10,0.,0
O,17,RNO,4,A1,10,180.,0
N,6,RCN1,12,90.,1,180.,0
O,20,RNO,6,A1,12,0.,0
O,20,RNO,6,A1,12,180.,0
N,3,RCN2,9,90.,1,180.,0
H,23,RNH,3,A2,9,0.,0
H,23,RNH,3,A2,9,180.,0
N,5,RCN2,11,90.,1,180.,0
H,26,RNH,5,A2,11,0.,0
H,26,RNH,5,A2,11,180.,0
N,7,RCN2,13,90.,1,180.,0
H,29,RNH,7,A2,13,0.,0
H,29,RNH,7,A2,13,180.,0
RC1=1.431682
RC2=1.451892
RCN1=1.431748
RNO=1.205098
A1=120.501393
RCN2=1.312086
RNH=0.990828
A2=118.920716
+++
title = "Gaussan-09 Example"
weight = "100"
+++
Gaussan-09 Example
--------------------------------------
{{< readfile file="content/submitting_jobs/app_specific/job-examples/gaussian/09/README.md" markdown="true" >}}
{{%attachments title="Related files" style="orange" /%}}
Slurm submission script for Gaussain-09 job across multiple nodes.
#!/bin/bash
#SBATCH -J g16
#SBATCH --nodes=1 --ntasks-per-node=4
#SBATCH --mem-per-cpu=2000
#SBATCH --time=10:00:00
#SBATCH --partition=batch
#SBATCH --error=TestJob.stderr
#SBATCH --output=TestJob.stdout
nodelist > ./machines.LINUX
echo $SLURM_JOB_ID > ./jobid
module load gaussian/16/RevA
source ${g16root}/g16/bsd/g16.profile
export GAUSS_SCRDIR=$TMPDIR
g16 test_g98.com
#g16 au3O2-c13-pbepbegd3iop30-opt-tz.gjf
%nprocs=4
#P RHF/6-31G** scf=direct test prop=fit
Gaussian Test Job 178:
TATB rhf/6-31g**//hf/6-31g**
Energy with tight cutoffs would be -1006.2213391, is -1006.2213170 with
default cutoffs
0,1
X
C,1,RC1
C,1,RC2,2,60.
C,1,RC1,3,60.,2,180.,0
C,1,RC2,4,60.,3,180.,0
C,1,RC1,5,60.,4,180.,0
C,1,RC2,6,60.,5,180.,0
X,2,1.,1,90.,3,0.,0
X,3,1.,1,90.,4,0.,0
X,4,1.,1,90.,5,0.,0
X,5,1.,1,90.,6,0.,0
X,6,1.,1,90.,7,0.,0
X,7,1.,1,90.,2,0.,0
N,2,RCN1,8,90.,1,180.,0
O,14,RNO,2,A1,8,0.,0
O,14,RNO,2,A1,8,180.,0
N,4,RCN1,10,90.,1,180.,0
O,17,RNO,4,A1,10,0.,0
O,17,RNO,4,A1,10,180.,0
N,6,RCN1,12,90.,1,180.,0
O,20,RNO,6,A1,12,0.,0
O,20,RNO,6,A1,12,180.,0
N,3,RCN2,9,90.,1,180.,0
H,23,RNH,3,A2,9,0.,0
H,23,RNH,3,A2,9,180.,0
N,5,RCN2,11,90.,1,180.,0
H,26,RNH,5,A2,11,0.,0
H,26,RNH,5,A2,11,180.,0
N,7,RCN2,13,90.,1,180.,0
H,29,RNH,7,A2,13,0.,0
H,29,RNH,7,A2,13,180.,0
RC1=1.431682
RC2=1.451892
RCN1=1.431748
RNO=1.205098
A1=120.501393
RCN2=1.312086
RNH=0.990828
A2=118.920716
+++
title = "Gaussan-16 Example"
weight = "100"
+++
Gaussan-16 Example
--------------------------------------
{{< readfile file="content/submitting_jobs/app_specific/job-examples/gaussian/16/README.md" markdown="true" >}}
{{%attachments title="Related files" style="orange" /%}}
Slurm submission script for Gaussain-16 job across multiple nodes.
Gromacs submission script for gromacs job across multiple nodes.
#!/bin/bash
#SBATCH --time=00:30:00
#SBATCH --mem-per-cpu=4096
#SBATCH --ntasks-per-node=1
#SBATCH --job-name=gromacs_gpu
#SBATCH --partition=gpu
#SBATCH --gres=gpu
#SBATCH --error=gromacs_gpu.stderr
#SBATCH --output=gromacs_gpu.stdout
module load compiler/gcc/7.1 gromacs-gpu/2020.1
gmx mdrun -nt 1 -nb gpu -pme gpu -bonded gpu
#!/bin/bash
#SBATCH --time=01:00:00
#SBATCH --mem-per-cpu=4096
#SBATCH --ntasks-per-node=1
#SBATCH --job-name=gromacs_mpi
#SBATCH --error=gromacs_mpi.stderr
#SBATCH --output=gromacs_mpi.stdout
module load compiler/gcc/9.1 openmpi/4.0 gromacs/2020.1
mpirun mdrun
;
; File 'mdout.mdp' was generated
; By user: eric (4228)
; On host: login.crane.hcc.unl.edu
; At date: Mon Sep 9 15:08:55 2019
;
; Created by:
; :-) GROMACS - gmx grompp, 2019.3 (-:
;
; Executable: /work/swanson/eric/gromacs/bin/gmx
; Data prefix: /work/swanson/eric/gromacs
; Working dir: /lustre/work/swanson/eric/gromacs/rnase_cubic
; Command line:
; gmx grompp -f pme_verlet.mdp
; VARIOUS PREPROCESSING OPTIONS
; Preprocessor information: use cpp syntax.
; e.g.: -I/home/joe/doe -I/home/mary/roe
include =
; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)
define =
; RUN CONTROL PARAMETERS
integrator = md
; Start time and timestep in ps
tinit = 0
dt = 0.002
nsteps = 100000
; For exact run continuation or redoing part of a run
init-step = 0
; Part index is updated automatically on checkpointing (keeps files separate)
simulation-part = 1
; mode for center of mass motion removal
comm-mode = Linear
; number of steps for center of mass motion removal
nstcomm = 100
; group(s) for center of mass motion removal
comm-grps =
; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd-fric = 0
ld-seed = -1
; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol = 10
emstep = 0.01
; Max number of iterations in relax-shells
niter = 20
; Step size (ps^2) for minimization of flexible constraints
fcstep = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep = 1000
nbfgscorr = 10
; TEST PARTICLE INSERTION OPTIONS
rtpi = 0.05
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 0
nstvout = 0
nstfout = 0
; Output frequency for energies to log file and energy file
nstlog = 0
nstcalcenergy = 100
nstenergy = 500
; Output frequency and precision for .xtc file
nstxout-compressed = 0
compressed-x-precision = 1000
; This selects the subset of atoms for the compressed
; trajectory file. You can select multiple groups. By
; default, all atoms will be written.
compressed-x-grps =
; Selection of energy groups
energygrps =
; NEIGHBORSEARCHING PARAMETERS
; cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)
cutoff-scheme = verlet
; nblist update frequency
nstlist = 10
; ns algorithm (simple or grid)
ns_type = grid
; Periodic boundary conditions: xyz, no, xy
pbc = xyz
periodic-molecules = no
; Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,
; a value of -1 means: use rlist
verlet-buffer-tolerance = 0.005
; nblist cut-off
rlist = 0.9
; long-range cut-off for switched potentials
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME
coulomb-modifier = Potential-shift-Verlet
rcoulomb-switch = 0
rcoulomb = 0.9
; Relative dielectric constant for the medium and the reaction field
epsilon-r = 1
epsilon-rf = 0
; Method for doing Van der Waals
vdw-type = Cut-off
vdw-modifier = Potential-shift-Verlet
; cut-off lengths
rvdw-switch = 0
rvdw = 0.9
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = No
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1
; Separate tables between energy group pairs
energygrp-table =
; Spacing for the PME/PPPM FFT grid
fourier_spacing = 0.1125
; FFT grid size, when a value is 0 fourierspacing will be used
fourier-nx = 0
fourier-ny = 0
fourier-nz = 0
; EWALD/PME/PPPM parameters
pme-order = 4
ewald-rtol = 1e-05
ewald-rtol-lj = 0.001
lj-pme-comb-rule = Geometric
ewald-geometry = 3d
epsilon-surface = 0
implicit-solvent = no
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl = v-rescale
nsttcouple = -1
nh-chain-length = 10
print-nose-hoover-chain-variables = no
; Groups to couple separately
tc_grps = system
; Time constant (ps) and reference temperature (K)
tau_t = 0.1
ref_t = 300
; pressure coupling
pcoupl = No
pcoupltype = Isotropic
nstpcouple = -1
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p = 1
compressibility =
ref-p =
; Scaling of reference coordinates, No, All or COM
refcoord-scaling = No
; OPTIONS FOR QMMM calculations
QMMM = no
; Groups treated Quantum Mechanically
QMMM-grps =
; QM method
QMmethod =
; QMMM scheme
QMMMscheme = normal
; QM basisset
QMbasis =
; QM charge
QMcharge =
; QM multiplicity
QMmult =
; Surface Hopping
SH =
; CAS space options
CASorbitals =
CASelectrons =
SAon =
SAoff =
SAsteps =
; Scale factor for MM charges
MMChargeScaleFactor = 1
; SIMULATED ANNEALING
; Type of annealing for each temperature group (no/single/periodic)
annealing =
; Number of time points to use for specifying annealing in each group
annealing-npoints =
; List of times at the annealing points for each group
annealing-time =
; Temp. at each annealing point, for each group.
annealing-temp =
; GENERATE VELOCITIES FOR STARTUP RUN
gen-vel = no
gen-temp = 300
gen-seed = -1
; OPTIONS FOR BONDS
constraints = all-bonds
; Type of constraint algorithm
constraint-algorithm = Lincs
; Do not constrain the start configuration
continuation = no
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR = no
; Relative tolerance of shake
shake-tol = 0.0001
; Highest order in the expansion of the constraint coupling matrix
lincs-order = 4
; Number of iterations in the final step of LINCS. 1 is fine for
; normal simulations, but use 2 to conserve energy in NVE runs.
; For energy minimization with constraints it should be 4 to 8.
lincs-iter = 1
; Lincs will write a warning to the stderr if in one step a bond
; rotates over more degrees than
lincs-warnangle = 30
; Convert harmonic bonds to morse potentials
morse = no
; ENERGY GROUP EXCLUSIONS
; Pairs of energy groups for which all non-bonded interactions are excluded
energygrp-excl =
; WALLS
; Number of walls, type, atom types, densities and box-z scale factor for Ewald
nwall = 0
wall-type = 9-3
wall-r-linpot = -1
wall-atomtype =
wall-density =
wall-ewald-zfac = 3
; COM PULLING
pull = no
; AWH biasing
awh = no
; ENFORCED ROTATION
; Enforced rotation: No or Yes
rotation = no
; Group to display and/or manipulate in interactive MD session
IMD-group =
; NMR refinement stuff
; Distance restraints type: No, Simple or Ensemble
disre = No
; Force weighting of pairs in one distance restraint: Conservative or Equal
disre-weighting = Conservative
; Use sqrt of the time averaged times the instantaneous violation
disre-mixed = no
disre-fc = 1000
disre-tau = 0
; Output frequency for pair distances to energy file
nstdisreout = 100
; Orientation restraints: No or Yes
orire = no
; Orientation restraints force constant and tau for time averaging
orire-fc = 0
orire-tau = 0
orire-fitgrp =
; Output frequency for trace(SD) and S to energy file
nstorireout = 100
; Free energy variables
free-energy = no
couple-moltype =
couple-lambda0 = vdw-q
couple-lambda1 = vdw-q
couple-intramol = no
init-lambda = -1
init-lambda-state = -1
delta-lambda = 0
nstdhdl = 50
fep-lambdas =
mass-lambdas =
coul-lambdas =
vdw-lambdas =
bonded-lambdas =
restraint-lambdas =
temperature-lambdas =
calc-lambda-neighbors = 1
init-lambda-weights =
dhdl-print-energy = no
sc-alpha = 0
sc-power = 1
sc-r-power = 6
sc-sigma = 0.3
sc-coul = no
separate-dhdl-file = yes
dhdl-derivatives = yes
dh_hist_size = 0
dh_hist_spacing = 0.1
; Non-equilibrium MD stuff
acc-grps =
accelerate =
freezegrps =
freezedim =
cos-acceleration = 0
deform =
; simulated tempering variables
simulated-tempering = no
simulated-tempering-scaling = geometric
sim-temp-low = 300
sim-temp-high = 300
; Ion/water position swapping for computational electrophysiology setups
; Swap positions along direction: no, X, Y, Z